• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.161-168
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• 2000

Plasmid pLEX3 isolated from the recombinant cosmid library of Zoogloea ramigera 115 was found to be responsible for the restoration of the rugose colony phenotype. To confirm the essential region responsible for the complementation, subclones were constructed from plasmid pLEX3 and transformed into mutant strain Z. ramigera 115SLR. The recombinant plasmids pLEX10 and pLEX11 were shown to complement the slime-forming property of Z. ramigera 115SLR. In a compositional analysis of the exopolysaccharides from Z. ramigera 115, Z. ramigera 115SLR, and Z. ramigera 115SLR harboring plasmid pLEX11, the exopolysaccharides showed a similar composition with glucose, galactose, and side chain groups. The complete nucleotide sequence of the 3.25kb genocim DNA insert in plasmid pLEX11 was determined and its analysis identified two open reading frames which could encode two proteins. The gene products derived form the two open reading frames were confirmed by and in vivo transcription using a T7-RNA polymerase. The ORF1 produced a 30 kDa protein, whereas the ORF2 was found responsible for the complementation of the morphological mutation and produced a 14 kDa protein. An in vivo gene expression of plasmid pTEX10 showed another open reading frame encoding a 50 kDa protein. The gene products form ORF1 and ORF2 are regarded as novel proteins which do not show any homology with other proteins.

• The Journal of the Korea Contents Association
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• v.11 no.3
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• pp.65-72
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• 2011

We stand at real world that some practical use method of gene information appears in succession by entrance on the stage of advanced techonlogy. As a lot of studies and development are achieved based on analysis of bio data, necessity of a tool that can help correct interpretation of data is required more and more in a lot of targets of bioinformatics to search new relation and information are established. In this paper, we are offered in existing I wish to offer user a more convenient study tool developing system that can supplement shortcomings of various tools for data analysis. So we've designed to offer in united environment that is not environment that is parted ORF driving out, bio information retrieval and work of similarity comparison lamp to work for bio data analysis and offers lacking consecutiveness in existing analysis system.

• Korean journal of applied entomology
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• v.32 no.3
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• pp.300-306
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• 1993

The CryIIA gene encoding the insecticidal crystal protein of Bacillus thuringiens!s subsp. kurstalri HD-l has been cloned in Escherichia col!, and its nucleotide sequences were determined completely. 5kb Hindlli fragment harboring CryIIA gene was screened in the large ca. 225kb plasmid DNA by southern blot. HindlIT digested 5kb fragment was ligated into pUC19 and transformed in E. coli. The 4kb BamHI-HindlIT fragment containing the CryIIA gene was subcloned and named pSKIIA. DNA sequence analysis demonstrates that pSKIIA is the gene of an operon which is comprised of Lhree open reading frames (designated orn, orf2 and or£3). The CrylIA gene is composed of 3,952bp-long BamHI-Hindill DNA restriction fragment. The orf3 code for a polypeptide of 633 amino acid residues. The protoxin protein has a predicted molecular weight of 70,780. The E. coli derived protoxin gene product is biologICally active against three species of Lepidopteran (Plu.lelia maculipennis, He/iolhis assulta, Spodoptera litura) and a species of Dip Leran( Culex pipines) larvae in bioassay.

• Journal of Microbiology
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• v.37 no.2
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• pp.102-110
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• 1999

Genetic determinant for the secondary metabolism was studied in heterologous expression in Streptomyces lividans TK-24 using Streptomyces griseus ATCC 10137 as a donor strain. Chromosomal DNA of S. griseus was ligated into the high-copy number Streptomyces shuttle plasmid, pWHM3, and introduced into S. lividans TK-24. A plasmid clone with 4.3-kb BamHI DNA of S. griseus (pMJJ201) was isolated by detecting for stimulatory effect on actinorhodin production by visual inspection. The 4.3-kb BamHI DNA was cloned into pWHM3 under the control of the strong constitutive ermEp promoter in both directions (pMJJ202); ermEp promoter-mediated transcription for coding sequence reading right to left: pMJJ203; ermEp promoter-mediated transcription for coding sequence reading left to right) and reintroduced into S. lividans TK-24. The production of actinorhodin was markedly stimulated due to introduction of pMJJ202 on regeneration agar. The introduction of pMJJ202 also stimulated production of actinorhodin and undecylproidigiosin in submerged culture employing the actinorhodin production medium. Introduction of pMJJ203 resulted in a marked decrease of production of the two pigments. Nucleotide sequence analysis of the 4.3-kb region revealed three coding sequences: two coding sequences reading left to right, ORF1 and ORF2, one coding sequence reading right to left, ORF3. Therefore, it was suggested that the ORF3 product was responsible for the stimulation of antibiotic production. The C-terminal region of ORF3 product showed a local alignment with Myb-related transcriptional factors, which implicated that the ORF3 product might be a novel DNA-binding protein related to the regulation of secondary metabolism in Streptomyces.

• The Plant Pathology Journal
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• v.34 no.2
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• pp.150-156
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• 2018

The genome sequences of two novel monopartite RNA viruses were identified in a common eelgrass (Zostera marina) transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these two novel viruses belong to the genus Amalgavirus in the family Amalgaviridae. They were named Zostera marina amalgavirus 1 (ZmAV1) and Zostera marina amalgavirus 2 (ZmAV2). Genomes of both ZmAV1 and ZmAV2 contain two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. The fusion protein (ORF1+2) of ORF1 and ORF2, which mediates RNA replication, was produced using the +1 programmed ribosomal frameshifting (PRF) mechanism. The +1 PRF motif sequence, UUU_CGN, which is highly conserved among known amalgaviruses, was also found in ZmAV1 and ZmAV2. Multiple sequence alignment of the ORF1+2 fusion proteins from 24 amalgaviruses revealed that +1 PRF occurred only at three different positions within the 13-amino acid-long segment, which was surrounded by highly conserved regions on both sides. This suggested that the +1 PRF may be constrained by the structure of fusion proteins. Genome sequences of ZmAV1 and ZmAV2, which are the first viruses to be identified in common eelgrass, will serve as useful resources for studying evolution and diversity of amalgaviruses.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.292-300
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• 2003

Pseudomonas fluorescens B16 is a plant glowth-prornoting rhizobacterium, which produces an antibacterial compound that is effective against plant root pathogens, such as Agrobacrerium tumefaciens and Raistonia solanacearum. We mutagenized the strain B16 with Omegon-Km and isolated six antibacterial-activity-deficient mutants. Two cosmid clones that hybridized with the mutant clones also were isolated from a genomic library of tile parent strain. Using deletion and complementation analyses, it was found that the biosynthesis genes resided in a 4.3-kb SalI-NarI fragment. When a plasmid clone carrying the fragment was introduced into P. fluorescens strain 1855.344, which does not exhibit any antibacterial activity, the transconjugants exhibited antibacterial activity, indicating that the plasmid clone carried all the genes essential for production of the antibacterial compound. DNA sequence analysis of the fragment identified four putative open reading frames (ORFs): orf1 through orf4 The deduced amino acid sequences of ORF1, ORF2, and ORF4 were similar to cystathionine gamma lyase, pyruvate formate-lyase activating enzyme, and transcriptional regulator, respectively, yet the amino acid sequence of ORF3 showed no similarities to any known proteins. It was also demonstrated that the antibacterial activity was responsible for biological control of the bacterial wilt caused by R. solanacearum.

• Korean journal of applied entomology
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• v.61 no.3
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• pp.449-460
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• 2022

The morphology and whole genome sequence of Spodoptera exigua nucleopolyhedrovirus K1 (SeNPV-K1) isolated in Korea were analyzed for the use as an eco-friendly control source against S. exigua. The polyhedra of SeNPV-K1 was amorphous with a size of 0.6-1.8 ㎛, and there was no external difference with the previously reported SeNPV. As a result of analyzing the nucleotide sequence of the whole genome, it was composed of 135,756 bp, which is 145 bp more than that of the previously reported SeNPV. The G+CG+C content was 44% and there were 6 homologous repeated sequences, so there was no significant difference from the previous report. As a result of ORF analysis, SeNPV-K1 had 137, two fewer than those previously reported, and 4 ORFs present only in SeNPV-K1 were confirmed. These 4 ORFs are non-essential genes and were not considered to have a significant influence on the characteristics of the SeNPV. The genome vista analysis showed that the overall sequence similarity between SeNPV-K1 and the previously reported SeNPV was very high. The whole genome of SeNPV-K1 analyzed for the first time in Korea was found to be similar to the previously reported SeNPV, but it was confirmed that it was a novel resource in Korea with different isolate.

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.264-269
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• 1994

To determine the nucleotide sequence of the ds RNA segment B containing the RNA dependent RNA polymerase (RdRp) gene of the DRT strain of infectious pancreatic necrosis virus (lPNV), the cDNA of the ds RNA segment B of the DRT strain of IPNV was synthesized using the reverse transcriptase (RT)-polymerase chain reaction (PCR) and its cDNA nucleotide sequence was determined. The DRT segment B was 2, 783 bp long and contained only a single long open reading frame (ORF) of 2, 535 bp in length. This ORF nucleotides encoded the VPl protein, the putative RdRp of IPNV. The VPl protein comsisted of 845 amino acids. The molecular weight of the RdRp, as deduced from the nucleotide sequence, is 94, 426. The nucleotide sequence of the ORF of the DRT showed 89.7% homology to the Jasper strain, but 80.8% to the Sp strain. The amino acid sequence of the ORF of the DRT sho.wed 97.6% homology to the Jasper strain, but 88.7% to the Sp strain. The conserved GTP-binding motif was detected in VPl protein.

• Journal of the Korean Chemical Society
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• v.48 no.5
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• pp.483-490
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• 2004

We have developed a novel polymerase chain reaction (PCR)-microchip gel electrophoresis (MGE) method based on the sieving gel mixture of commercially available poly(vinylpyrrolidone) (PVP) and hydroxy ethyl cellulose (HEC) for the rapid detection and diagnosis of the orf virus (ORFV) from Korean indigenous goat. After amplification of 594-bp DNA fragment from the B2L gene of ORF virus, the amplicon was analyzed by the MGE separation. The glass microfluidic chip (64 mm total length (36 mm effective length)${\times}$90 ${\mu}$m width${\times}$20 ${\mu}$m depth) allowed the fast detection and diagnosis of ORFV in the mixture of 1.0% PVP ($M_r$ 360,000) and 1.0% HEC ($M_r$250,000) as a sieving matrix with better resolution and reproducibility of DNA fragments. Under the electric field of 277.8 V/cm, the 594-bp DNA was analyzed within 4 min. Compared to traditional slab gel electrophoresis, the PCR-MGE method was twenty times faster and an effective clinical method for the quantitative analysis of ORFV.

• Korean Journal of Veterinary Research
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• v.58 no.3
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• pp.143-146
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• 2018

The capsid protein of porcine circovirus type 2 (PCV2) encoded by open reading frame 2 (ORF2) is important for neutralizing activity against PCV2 infection. This study investigated the heterogeneity of the ORF2 gene of PCV2 isolated in Korea during 2016-2017. The results revealed that PCV2d is currently the predominant genotype. Moreover, comparison of ORF2 from 17 PCV2 isolates revealed 88.3-100% homology at the nucleotide (deduced amino acid 86.3-100%) level. Interestingly, 61.5% (8/13) of the PCV2d isolates had glycine at position 210. These data provide a useful information for PCV2 epidemiology in Korea.